Update bootstrap to v2.2.2.

Keeping the custom changes in bootstrap.css needed for sphinx, and work around the navbar issue by using the same font as the old version.
remove the unneeded jquery-migrate.js
remove white background color for navbar and use bootstrap's default one
remove the unneeded affix
use the new default bootstrap font and make container's max-width bigger so that the navbar shows properly
trying to get the style close to the old one